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LOC123038167 Sharpr-MPRA regulatory region 13474 [ Homo sapiens (human) ]

Gene ID: 123038167, updated on 12-Sep-2024

Summary

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Gene symbol
LOC123038167
Gene description
Sharpr-MPRA regulatory region 13474
Gene type
biological region
Feature type(s)
regulatory: silencer
RefSeq status
REVIEWED
Organism
Homo sapiens
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Summary
This genomic sequence was predicted to be a transcriptional regulatory region based on chromatin state analysis from the ENCODE (ENCyclopedia Of DNA Elements) project. It was validated as a functional repressive element by the Sharpr-MPRA technique (Systematic high-resolution activation and repression profiling with reporter tiling using massively parallel reporter assays) in both HepG2 liver carcinoma cells (group: HepG2 Repressive non-DNase unmatched - State 14:Gen5', transcription transition, highly expressed genes towards 5' end) and K562 erythroleukemia cells (group: K562 Repressive DNase matched - State 13:Ctcf, distal CTCF/candidate insulator without open chromatin). [provided by RefSeq, Oct 2021]
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Genomic context

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See LOC123038167 in Genome Data Viewer
Location:
3q
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 3 NC_000003.12 (124995405..124995699)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 3 NC_060927.1 (127721017..127721311)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 3 NC_000003.11 (124714249..124714543)

Chromosome 3 - NC_000003.12Genomic Context describing neighboring genes Neighboring gene integrin subunit beta 5 Neighboring gene H3K27ac hESC enhancer GRCh37_chr3:124587550-124588050 Neighboring gene H3K27ac hESC enhancer GRCh37_chr3:124588051-124588551 Neighboring gene Sharpr-MPRA regulatory region 8988 Neighboring gene H3K27ac hESC enhancer GRCh37_chr3:124604052-124604936 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 14655 Neighboring gene enolase 1 pseudogene 3 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 14656 Neighboring gene NANOG-H3K27ac hESC enhancer GRCh37_chr3:124606705-124607587 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr3:124607588-124608472 Neighboring gene NANOG hESC enhancer GRCh37_chr3:124626617-124627118 Neighboring gene mucin 13, cell surface associated Neighboring gene heart development protein with EGF like domains 1 Neighboring gene MED14-independent group 3 enhancer GRCh37_chr3:124720175-124721374 Neighboring gene Sharpr-MPRA regulatory region 1791 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:124762717-124763230 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 20408 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 14657 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 14658 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 14659 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 14660 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 20409 Neighboring gene uncharacterized LOC124909423 Neighboring gene RNA, 5S ribosomal pseudogene 137

Genomic regions, transcripts, and products

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Go to nucleotide: Graphics FASTA GenBank

Bibliography

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Related articles in PubMed

  1. Genome-scale high-resolution mapping of activating and repressive nucleotides in regulatory regions. Ernst J, et al. Nat Biotechnol, 2016 Nov. PMID 27701403, Free PMC Article

GeneRIFs: Gene References Into Functions

Phenotypes

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Review eQTL and phenotype association data in this region using PheGenI

Variation

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See variants in ClinVar

See Variation Viewer (GRCh37.p13)

NCBI Reference Sequences (RefSeq)

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RefSeqs maintained independently of Annotated Genomes

These reference sequences exist independently of genome builds. Explain

These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

Genomic

  1. NG_077298.1 

    Range
    101..395
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2024_08

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference GRCh38.p14 Primary Assembly

Genomic

  1. NC_000003.12 Reference GRCh38.p14 Primary Assembly

    Range
    124995405..124995699
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060927.1 Alternate T2T-CHM13v2.0

    Range
    127721017..127721311
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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